Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.

Bacteriophage transfer (lysogenic conversion) promotes bacterial virulence evolution. There is limited understanding of the factors that determine lysogenic conversion dynamics within infected hosts. A murine Typhimurium (Tm) diarrhea model was used to study the transfer of SopEΦ, a prophage from Tm SL1344, toTm ATCC14028S. Gut inflammation and enteric disease triggered >55% lysogenic conversion of ATCC14028S within 3 days. Without inflammation, SopEΦ transfer was reduced by up to 10-fold. This was because inflammation (e.g., reactive oxygen species, reactive nitrogen species, hypochlorite) triggers the bacterial SOS response, boosts expression of the phage antirepressor Tum, and thereby promotes free phage production and subsequent transfer. Mucosal vaccination prevented a dense intestinal Tm population from inducing inflammation and consequently abolished SopEΦ transfer. Vaccination may be a general strategy for blocking pathogen evolution that requires disease-driven transfer of temperate bacteriophages.

Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.

BackgroundViral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.MethodsWe identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.ResultsWe show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.ConclusionSince IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0452-1) contains supplementary material, which is available to authorized users.

Temperate phages, the bacterial viruses able to enter in a dormant prophage state in bacterial genomes, are present in the majority of bacterial strains for which the genome sequence is available. Although these prophages are generally considered to increase their hosts’ fitness by bringing beneficial genes, studies demonstrating such effects in ecologically relevant environments are relatively limited to few bacterial species. Here, we investigated the impact of prophage carriage in the gastrointestinal tract of monoxenic mice. Combined with mathematical modelling, these experimental results provided a quantitative estimation of key parameters governing phage-bacteria interactions within this model ecosystem. We used wild-type and mutant strains of the best known host/phage pair, Escherichia coli and phage λ. Unexpectedly, λ prophage caused a significant fitness cost for its carrier, due to an induction rate 50-fold higher than in vitro, with 1 to 2% of the prophage being induced. However, when prophage carriers were in competition with isogenic phage susceptible bacteria, the prophage indirectly benefited its carrier by killing competitors: infection of susceptible bacteria led to phage lytic development in about 80% of cases. The remaining infected bacteria were lysogenized, resulting overall in the rapid lysogenization of the susceptible lineage. Moreover, our setup enabled to demonstrate that rare events of phage gene capture by homologous recombination occurred in the intestine of monoxenic mice. To our knowledge, this study constitutes the first quantitative characterization of temperate phage-bacteria interactions in a simplified gut environment. The high prophage induction rate detected reveals DNA damage-mediated SOS response in monoxenic mouse intestine. We propose that the mammalian gut, the most densely populated bacterial ecosystem on earth, might foster bacterial evolution through high temperate phage activity.

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The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering virus-like particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the Epoisses cheese virome. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems. IMPORTANCEWhether bacterial viruses (phages) are necessary or not to maintain food ecosystem function is not clear. They could play a negative role by killing cornerstone species that are necessary for fermentation. But they might also be positive players, by preventing the overgrowth of unwanted species (e.g. food spoilers). To assess phages contribution to food ecosystem functioning, it is essential to set up efficient procedures for extracting viral particles in solid .

12Running Head: Viral extraction procedure for cheese virome analysis 13 14 #Address correspondence to Eric Dugat-Bony, eric.dugat-bony@inra.fr 15 16 KEYWORDS 17 Cheese rind, viral metagenomic, VLPs extraction procedure 18 2 ABSTRACT 19The structure and functioning of microbial communities from fermented foods, including 20 cheese, have been extensively studied during the past decade. However, there is still a lack of 21 information about both the occurrence and the role of viruses in modulating the function of 22 this type of spatially structured and solid ecosystems. Viral metagenomics was recently 23 applied to a wide variety of environmental samples and standardized procedures for 24 recovering virus-like particles from different type of materials has emerged. In this study, we 25 adapted a procedure originally developed to extract viruses from fecal samples, in order to 26 enable efficient virome analysis of cheese surface. We tested and validated the positive 27 impact of both addition of a filtration step prior to virus concentration and substitution of 28 purification by density gradient ultracentrifugation by a simple chloroform treatment to 29 eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a 30 vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the 31 subsequent clusters assembled from the virome were analyzed to assess those belonging to 32 putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best 33 procedure was then chosen, and used to describe the Epoisses cheese virome. This study 34 provides the basis of future investigations regarding the ecological importance of viruses in 35 cheese microbial ecosystems.36 37 IMPORTANCE 38Whether bacterial viruses (phages) are necessary or not to maintain food ecosystem function 39 is not clear. They could play a negative role by killing cornerstone species that are necessary 40 for fermentation. But they might also be positive players, by preventing the overgrowth of 41 unwanted species (e.g. food spoilers). To assess phages contribution to food ecosystem 42 functioning, it is essential to set up efficient procedures for extracting viral particles in solid 43 3 food matrix, then selectively sequence their DNA without being contaminated by bacterial 44 DNA, and finally to find strategies to assemble their genome out of metagenomic sequences.45 This study, using cheese rind surface as a model, describes a comparative analysis of 46 procedures for selectively extracting viral DNA from cheese and to efficiently characterize 47 49The cheese surface hosts dense and diverse microbial communities composed of bacteria, 50 yeasts and filamentous fungi. Composition of these communities has been studied for decades 51 (see (1) and (2) for reviews). With the help of high throughput sequencing techniques, we 52 now have detailed pictures of the communities present in a large panel of cheese varieties, and 53 from all over the world (3-6). However, like many other microbia...